With VMDirectPath don't even try thinking about trying to get multiple VMs to talk to the same physical hardware, it'll either not work at all or not work stably.
Now onto your questions, with only three x 1Gbps NICs you'll see only minor performance gains by using VMDirectPath, and then really only in terms of latency, hardly any additional bandwidth. Using the regular vSwitch/port group method can saturate a single 10Gbps NIC and is easier to setup and manage and doesn't force compromises like VMDirectPath does such an losing vMotion ability. If you want the benefit of the second and third NICs simply add them to the vSwitch, cable them to your switch/es correctly and set the pathing policy - it's far easier than passing them through and teaming them in-VM.
Yes you can pass through your disks if you really want, either using physical mode or via VMDirectPath - if you use the latter you lose the whole controller to a single VM of course. And yes there would be a performance gain, I'd suggest somewhere between 5% and 25% overall depending on system. Again I wouldn't bother though, you're moving to virtualisation yet by using these techniques losing much of the benefits of doing so, I believe it's counter-productive.